Hi all,
I have bam file of whole exome human data. Now I want to check coverage of a list of genes in my data. Basically I want get output like this:
Gene Percentage of coding region covered
A1BG 100 %
A1BG-AS1 100%
A1CF 99.94%
NEK8 100%
FANCI 100%
A2ML1 100%
2 answers
Create a BED file of your genes of interests and then use mosdepth as described https://github.com/brentp/mosdepth#exome-example
A BED file is a tab separated file which defines a region. It has 3 columns, chromosome, start, end.
You could generate using the method pointed by @Trivas or using BioMart https://www.ensembl.org/biomart/martview
I have get this output by using mosdepth. It give me coverage at 1X, 5X,10X,15X ,20X , 30X. In some regions genes are repeated as you can see in the example. Now how Can i convert the coverage in the form of percentage?
example:
#chrom start end region id 1X 5X 10X 15X 20X 30X
chr1 69090 70008 OR4F5 918 918 918 918 918 918
chr1 134772 140566 LOC729737 1985 0 0 0 0 0
chr1 182387 184878 DDX11L17 2464 1214 860 550 412 273
chr1 187890 187958 MIR6859-1 68 68 68 68 68 68
chr1 1020119 1056114 AGRN 22418 15841 14836 14026 13286 12229
chr1 1020119 1056114 AGRN 22418 15841 14836 14026 13286 12229
chr1 1033992 1056114 AGRN 17233 14700 13867 13225 12695 11715
I have get this output by using mosdepth. It give me coverage at 1X, 5X,10X,15X ,20X , 30X. In some regions genes are repeated as you can see in the example. Now how Can i convert the coverage in the form of percentage?
example:
chrom start end region 1X 5X 10X 15X 20X 30X
chr1 69090 70008 OR4F5 918 918 918 918 918 918
chr1 134772 140566 LOC729737 1985 0 0 0 0 0
chr1 182387 184878 DDX11L17 2464 1214 860 550 412 273
chr1 187890 187958 MIR6859-1 68 68 68 68 68 68
chr1 1020119 1056114 AGRN 22418 15841 14836 14026 13286 12229
chr1 1020119 1056114 AGRN 22418 15841 14836 14026 13286 12229
chr1 1033992 1056114 AGRN 17233 14700 13867 13225 12695 11715
This may be useful https://github.com/brentp/mosdepth/issues/166#issuecomment-993250933
Log in to answer this question.
-
Calculate coverage per gene
written by anii •
-
From where i can download the bed file of hg19 which contaning the corrdinates as well as gene name.
written by anii •
-
Retrieve transcription factors from gene set using biomaRt
written by melissachua90 •
-
Multiple identical mutations in SnpEff result: ex1.genes.txt
written by Maya •
-
gene expression data of scRNA-Seq
written by jabbari.parnian •
-
soft threshold for co-expression analysis using WGCNA based on scale independence
written by newbie
-
Hi blog how to calculate differntial expression analysis if thre is no replicates in count data usi…
written by gskbioinfo143 •
-
How Coverage percentage is calculated in NGS data
written by crivenster
-
Question In Normalizing With Ercc Spike-In Control
written by camelbbs
-
1000Genome Project To Cover Gc-Rich Region?
written by michealsmith
If this data is using a specific kit then the manufacturer may have the BED files available for the regions that are covered by the kit. You should use that file.
Yes, they used the Agilent kit and i have downloaded the bed file from the agilent site. should i use this bed file or should i get the file from the manufacture?
Use the agilent file. Make sure it is for the genome build you are using otherwise things would be totally off.
Okay , Thakyou GenoMax